Starting phenix.real_space_refine on Wed Mar 4 02:23:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ki1_22883/03_2026/7ki1_22883.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ki1_22883/03_2026/7ki1_22883.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ki1_22883/03_2026/7ki1_22883.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ki1_22883/03_2026/7ki1_22883.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ki1_22883/03_2026/7ki1_22883.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ki1_22883/03_2026/7ki1_22883.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 6497 2.51 5 N 1755 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10265 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2772 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 4, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3186 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 370} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 236 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.39, per 1000 atoms: 0.23 Number of scatterers: 10265 At special positions: 0 Unit cell: (92.939, 184.671, 102.595, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1954 8.00 N 1755 7.00 C 6497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.04 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 547.4 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 45.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.509A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.518A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.633A pdb=" N THR A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.663A pdb=" N GLU A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 removed outlier: 3.603A pdb=" N CYS A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.623A pdb=" N LYS A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.586A pdb=" N CYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.513A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 279 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 306 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.564A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.513A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 22 removed outlier: 3.627A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.634A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.597A pdb=" N SER R 49 " --> pdb=" O GLN R 45 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 93 removed outlier: 4.482A pdb=" N SER R 93 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 141 Processing helix chain 'R' and resid 142 through 169 removed outlier: 3.561A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 Processing helix chain 'R' and resid 174 through 198 Processing helix chain 'R' and resid 200 through 205 Processing helix chain 'R' and resid 215 through 223 Processing helix chain 'R' and resid 223 through 256 removed outlier: 3.774A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN R 234 " --> pdb=" O PHE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 274 removed outlier: 3.645A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 Proline residue: R 283 - end of helix removed outlier: 3.504A pdb=" N VAL R 287 " --> pdb=" O PRO R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 294 through 298 Processing helix chain 'R' and resid 306 through 338 Proline residue: R 312 - end of helix removed outlier: 3.794A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN R 338 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 366 removed outlier: 3.748A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 380 Processing helix chain 'R' and resid 381 through 403 removed outlier: 3.977A pdb=" N PHE R 390 " --> pdb=" O THR R 386 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing helix chain 'P' and resid 8 through 36 removed outlier: 3.729A pdb=" N GLU P 27 " --> pdb=" O GLN P 23 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG P 36 " --> pdb=" O LEU P 32 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.456A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.541A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.938A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.907A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.557A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.754A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.514A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.942A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.669A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 Processing sheet with id=AB3, first strand: chain 'R' and resid 79 through 84 removed outlier: 3.773A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR R 101 " --> pdb=" O ASP R 122 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3270 1.34 - 1.46: 2055 1.46 - 1.58: 5018 1.58 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 10422 Sorted by residual: bond pdb=" C LEU R 118 " pdb=" N PRO R 119 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.34e-02 5.57e+03 1.50e+01 bond pdb=" C ASP R 293 " pdb=" N GLU R 294 " ideal model delta sigma weight residual 1.331 1.281 0.050 1.33e-02 5.65e+03 1.44e+01 bond pdb=" C ARG R 421 " pdb=" N LEU R 422 " ideal model delta sigma weight residual 1.334 1.288 0.047 1.27e-02 6.20e+03 1.36e+01 bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.332 1.380 -0.048 1.34e-02 5.57e+03 1.30e+01 bond pdb=" C LEU R 422 " pdb=" N GLU R 423 " ideal model delta sigma weight residual 1.329 1.377 -0.048 1.40e-02 5.10e+03 1.20e+01 ... (remaining 10417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 13139 1.77 - 3.53: 889 3.53 - 5.30: 93 5.30 - 7.06: 19 7.06 - 8.83: 2 Bond angle restraints: 14142 Sorted by residual: angle pdb=" N PHE R 381 " pdb=" CA PHE R 381 " pdb=" C PHE R 381 " ideal model delta sigma weight residual 111.96 103.13 8.83 1.41e+00 5.03e-01 3.92e+01 angle pdb=" N PHE R 143 " pdb=" CA PHE R 143 " pdb=" C PHE R 143 " ideal model delta sigma weight residual 111.28 104.99 6.29 1.09e+00 8.42e-01 3.33e+01 angle pdb=" N TYR R 305 " pdb=" CA TYR R 305 " pdb=" C TYR R 305 " ideal model delta sigma weight residual 113.50 106.68 6.82 1.23e+00 6.61e-01 3.07e+01 angle pdb=" N ARG R 380 " pdb=" CA ARG R 380 " pdb=" C ARG R 380 " ideal model delta sigma weight residual 113.17 106.33 6.84 1.26e+00 6.30e-01 2.94e+01 angle pdb=" C ASP B 38 " pdb=" N PRO B 39 " pdb=" CA PRO B 39 " ideal model delta sigma weight residual 119.78 124.91 -5.13 1.03e+00 9.43e-01 2.48e+01 ... (remaining 14137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5509 17.82 - 35.63: 495 35.63 - 53.45: 137 53.45 - 71.27: 28 71.27 - 89.08: 12 Dihedral angle restraints: 6181 sinusoidal: 2426 harmonic: 3755 Sorted by residual: dihedral pdb=" CB CYS R 85 " pdb=" SG CYS R 85 " pdb=" SG CYS R 126 " pdb=" CB CYS R 126 " ideal model delta sinusoidal sigma weight residual 93.00 171.19 -78.19 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -148.30 62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -150.91 -29.09 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1247 0.068 - 0.137: 260 0.137 - 0.205: 47 0.205 - 0.273: 6 0.273 - 0.341: 4 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA GLU R 128 " pdb=" N GLU R 128 " pdb=" C GLU R 128 " pdb=" CB GLU R 128 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ARG R 376 " pdb=" N ARG R 376 " pdb=" C ARG R 376 " pdb=" CB ARG R 376 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA VAL R 370 " pdb=" N VAL R 370 " pdb=" C VAL R 370 " pdb=" CB VAL R 370 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1561 not shown) Planarity restraints: 1805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR P 19 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C TYR P 19 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR P 19 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU P 20 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 141 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C LEU R 141 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU R 141 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU R 142 " 0.012 2.00e-02 2.50e+03 ... (remaining 1802 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2429 2.79 - 3.31: 9798 3.31 - 3.84: 17356 3.84 - 4.37: 22184 4.37 - 4.90: 35911 Nonbonded interactions: 87678 Sorted by model distance: nonbonded pdb=" O SER A 51 " pdb=" ND2 ASN A 292 " model vdw 2.257 3.120 nonbonded pdb=" N ARG R 64 " pdb=" OD1 ASP R 74 " model vdw 2.284 3.120 nonbonded pdb=" O THR A 325 " pdb=" OG1 THR A 325 " model vdw 2.296 3.040 nonbonded pdb=" O ASN R 115 " pdb=" OG SER R 116 " model vdw 2.321 3.040 nonbonded pdb=" O HOH R 506 " pdb=" O HOH R 507 " model vdw 2.322 3.040 ... (remaining 87673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.990 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 10429 Z= 0.476 Angle : 0.933 8.830 14154 Z= 0.633 Chirality : 0.061 0.341 1564 Planarity : 0.005 0.056 1805 Dihedral : 15.536 89.084 3733 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.28 % Allowed : 12.56 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.22), residues: 1261 helix: -1.58 (0.20), residues: 532 sheet: -0.20 (0.31), residues: 228 loop : -0.69 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 102 TYR 0.024 0.003 TYR R 69 PHE 0.022 0.002 PHE B 151 TRP 0.014 0.002 TRP N 47 HIS 0.008 0.002 HIS R 99 Details of bonding type rmsd covalent geometry : bond 0.00810 (10422) covalent geometry : angle 0.93138 (14142) SS BOND : bond 0.00403 ( 6) SS BOND : angle 2.27192 ( 12) hydrogen bonds : bond 0.25289 ( 492) hydrogen bonds : angle 8.57363 ( 1392) Misc. bond : bond 0.09276 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.405 Fit side-chains REVERT: B 23 LYS cc_start: 0.8124 (tttp) cc_final: 0.7912 (tttm) REVERT: B 217 MET cc_start: 0.7777 (ppp) cc_final: 0.7420 (pmm) outliers start: 3 outliers final: 1 residues processed: 153 average time/residue: 0.7403 time to fit residues: 119.7487 Evaluate side-chains 131 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 13 GLN R 182 ASN R 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.199546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.111373 restraints weight = 10066.034| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.82 r_work: 0.2981 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10429 Z= 0.147 Angle : 0.594 6.063 14154 Z= 0.325 Chirality : 0.042 0.157 1564 Planarity : 0.005 0.058 1805 Dihedral : 5.398 52.356 1405 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 13.67 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.22), residues: 1261 helix: 0.23 (0.22), residues: 536 sheet: -0.03 (0.32), residues: 228 loop : -0.49 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 299 TYR 0.023 0.002 TYR R 148 PHE 0.017 0.002 PHE A 212 TRP 0.028 0.002 TRP R 39 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00313 (10422) covalent geometry : angle 0.59315 (14142) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.34625 ( 12) hydrogen bonds : bond 0.05257 ( 492) hydrogen bonds : angle 4.84155 ( 1392) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7902 (pptt) cc_final: 0.7194 (ptpt) REVERT: A 392 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8616 (mt-10) REVERT: B 23 LYS cc_start: 0.8204 (tttp) cc_final: 0.7686 (tmtm) REVERT: B 44 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: B 146 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8704 (tp) REVERT: B 197 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8583 (mtm110) REVERT: B 217 MET cc_start: 0.8692 (ppp) cc_final: 0.8380 (pmm) REVERT: B 298 ASP cc_start: 0.9153 (t0) cc_final: 0.8945 (t0) REVERT: G 36 ASP cc_start: 0.8498 (m-30) cc_final: 0.8252 (m-30) REVERT: G 37 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8443 (mp) REVERT: R 41 GLU cc_start: 0.6003 (mm-30) cc_final: 0.5471 (tt0) REVERT: R 232 LEU cc_start: 0.7256 (tp) cc_final: 0.6670 (mm) REVERT: R 262 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5818 (tp30) REVERT: R 303 MET cc_start: 0.7550 (mmt) cc_final: 0.7275 (tpt) REVERT: P 9 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6499 (mp0) outliers start: 26 outliers final: 8 residues processed: 156 average time/residue: 0.6987 time to fit residues: 115.8597 Evaluate side-chains 135 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 118 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 36 ASN B 155 ASN R 112 GLN R 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.197521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108952 restraints weight = 10030.970| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.99 r_work: 0.2928 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10429 Z= 0.217 Angle : 0.614 7.058 14154 Z= 0.334 Chirality : 0.045 0.151 1564 Planarity : 0.005 0.062 1805 Dihedral : 5.283 32.931 1403 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.32 % Allowed : 14.13 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1261 helix: 0.76 (0.22), residues: 535 sheet: 0.05 (0.31), residues: 229 loop : -0.44 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.022 0.002 TYR R 148 PHE 0.016 0.002 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.002 HIS R 180 Details of bonding type rmsd covalent geometry : bond 0.00487 (10422) covalent geometry : angle 0.61290 (14142) SS BOND : bond 0.00469 ( 6) SS BOND : angle 1.14591 ( 12) hydrogen bonds : bond 0.05247 ( 492) hydrogen bonds : angle 4.61858 ( 1392) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7828 (pptt) cc_final: 0.7140 (ptpt) REVERT: A 203 LEU cc_start: 0.5015 (OUTLIER) cc_final: 0.4185 (tt) REVERT: B 23 LYS cc_start: 0.8178 (tttp) cc_final: 0.7659 (tttm) REVERT: B 42 ARG cc_start: 0.7679 (tpt170) cc_final: 0.7322 (tpt170) REVERT: B 44 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: B 59 TYR cc_start: 0.9287 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 146 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8739 (tp) REVERT: B 197 ARG cc_start: 0.8890 (mtp180) cc_final: 0.8641 (mtm110) REVERT: B 217 MET cc_start: 0.8775 (ppp) cc_final: 0.8426 (pmm) REVERT: B 298 ASP cc_start: 0.9126 (t0) cc_final: 0.8894 (t0) REVERT: B 340 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8280 (m-40) REVERT: G 36 ASP cc_start: 0.8612 (m-30) cc_final: 0.8343 (m-30) REVERT: G 37 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8494 (mp) REVERT: R 41 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5752 (tt0) REVERT: R 262 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6099 (tp30) REVERT: R 292 GLU cc_start: 0.6900 (tt0) cc_final: 0.6641 (tp30) REVERT: R 303 MET cc_start: 0.7699 (mmt) cc_final: 0.7468 (tpt) REVERT: R 407 ASN cc_start: 0.8134 (OUTLIER) cc_final: 0.7764 (m-40) REVERT: P 9 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6334 (mp0) outliers start: 36 outliers final: 14 residues processed: 157 average time/residue: 0.6862 time to fit residues: 114.3913 Evaluate side-chains 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 9 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 231 LEU Chi-restraints excluded: chain R residue 262 GLU Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 98 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.0000 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.0060 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.201441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113947 restraints weight = 10155.730| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.84 r_work: 0.3050 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10429 Z= 0.105 Angle : 0.491 5.757 14154 Z= 0.267 Chirality : 0.040 0.153 1564 Planarity : 0.004 0.062 1805 Dihedral : 4.652 30.392 1403 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.95 % Allowed : 15.51 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1261 helix: 1.35 (0.23), residues: 536 sheet: 0.27 (0.32), residues: 228 loop : -0.28 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.018 0.001 TYR R 148 PHE 0.014 0.001 PHE A 212 TRP 0.020 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00221 (10422) covalent geometry : angle 0.49008 (14142) SS BOND : bond 0.00278 ( 6) SS BOND : angle 1.07890 ( 12) hydrogen bonds : bond 0.03884 ( 492) hydrogen bonds : angle 4.18041 ( 1392) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6851 (pt0) cc_final: 0.6195 (pp20) REVERT: A 17 LYS cc_start: 0.7788 (pptt) cc_final: 0.7101 (ptpt) REVERT: A 203 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.3958 (tt) REVERT: A 392 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8473 (mt-10) REVERT: B 15 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7090 (ttmm) REVERT: B 23 LYS cc_start: 0.8164 (tttp) cc_final: 0.7654 (tmtm) REVERT: B 42 ARG cc_start: 0.7632 (tpt170) cc_final: 0.7274 (tpt170) REVERT: B 44 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7873 (mt0) REVERT: B 46 ARG cc_start: 0.8542 (mmt-90) cc_final: 0.8196 (mmp80) REVERT: B 59 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.7866 (t80) REVERT: B 134 ARG cc_start: 0.7871 (ptp-110) cc_final: 0.7046 (ppt170) REVERT: B 146 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8594 (tp) REVERT: B 155 ASN cc_start: 0.8917 (t0) cc_final: 0.8680 (t0) REVERT: B 197 ARG cc_start: 0.8856 (mtp180) cc_final: 0.8645 (mtp85) REVERT: B 217 MET cc_start: 0.8735 (ppp) cc_final: 0.8370 (pmm) REVERT: B 298 ASP cc_start: 0.9118 (t0) cc_final: 0.8876 (t0) REVERT: B 340 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8464 (m-40) REVERT: G 36 ASP cc_start: 0.8569 (m-30) cc_final: 0.8210 (m-30) REVERT: R 41 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5776 (tt0) REVERT: R 221 GLN cc_start: 0.5559 (mt0) cc_final: 0.5358 (mt0) REVERT: P 9 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6408 (mp0) outliers start: 32 outliers final: 7 residues processed: 161 average time/residue: 0.6702 time to fit residues: 114.6637 Evaluate side-chains 145 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 86 optimal weight: 0.0020 chunk 87 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.200710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.112710 restraints weight = 10099.427| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.84 r_work: 0.3043 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10429 Z= 0.114 Angle : 0.499 4.953 14154 Z= 0.270 Chirality : 0.041 0.154 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.561 32.967 1403 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.86 % Allowed : 16.90 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1261 helix: 1.58 (0.23), residues: 535 sheet: 0.27 (0.32), residues: 228 loop : -0.24 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.020 0.001 TYR R 148 PHE 0.013 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00245 (10422) covalent geometry : angle 0.49790 (14142) SS BOND : bond 0.00244 ( 6) SS BOND : angle 1.31625 ( 12) hydrogen bonds : bond 0.03928 ( 492) hydrogen bonds : angle 4.05863 ( 1392) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6839 (pt0) cc_final: 0.6222 (pp20) REVERT: A 17 LYS cc_start: 0.7750 (pptt) cc_final: 0.7086 (ptpt) REVERT: A 203 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.3958 (tt) REVERT: A 392 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8544 (mt-10) REVERT: B 15 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7069 (ttmm) REVERT: B 23 LYS cc_start: 0.8161 (tttp) cc_final: 0.7635 (tmtm) REVERT: B 42 ARG cc_start: 0.7643 (tpt170) cc_final: 0.7249 (tpt170) REVERT: B 44 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: B 46 ARG cc_start: 0.8562 (mmt-90) cc_final: 0.8222 (mmp80) REVERT: B 59 TYR cc_start: 0.9230 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 134 ARG cc_start: 0.7873 (ptp-110) cc_final: 0.7224 (ppp80) REVERT: B 146 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8651 (tp) REVERT: B 155 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8651 (t0) REVERT: B 197 ARG cc_start: 0.8852 (mtp180) cc_final: 0.8630 (mtp85) REVERT: B 217 MET cc_start: 0.8809 (ppp) cc_final: 0.8439 (pmm) REVERT: B 298 ASP cc_start: 0.9069 (t0) cc_final: 0.8776 (t0) REVERT: B 340 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8328 (m110) REVERT: G 36 ASP cc_start: 0.8582 (m-30) cc_final: 0.8261 (m-30) REVERT: R 41 GLU cc_start: 0.6033 (mm-30) cc_final: 0.5607 (tt0) REVERT: R 376 ARG cc_start: 0.5548 (OUTLIER) cc_final: 0.4516 (mmp80) REVERT: R 407 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7791 (m-40) REVERT: R 418 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6442 (pt0) REVERT: P 9 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6359 (mp0) outliers start: 31 outliers final: 8 residues processed: 162 average time/residue: 0.6317 time to fit residues: 108.9371 Evaluate side-chains 153 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 20.0000 chunk 17 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 69 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.199851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.111687 restraints weight = 10114.048| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.03 r_work: 0.2987 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10429 Z= 0.140 Angle : 0.515 5.281 14154 Z= 0.279 Chirality : 0.042 0.152 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.638 33.609 1403 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.77 % Allowed : 17.27 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1261 helix: 1.65 (0.23), residues: 534 sheet: 0.23 (0.32), residues: 229 loop : -0.26 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.020 0.001 TYR R 148 PHE 0.014 0.001 PHE A 212 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00309 (10422) covalent geometry : angle 0.51470 (14142) SS BOND : bond 0.00286 ( 6) SS BOND : angle 1.10814 ( 12) hydrogen bonds : bond 0.04107 ( 492) hydrogen bonds : angle 4.10356 ( 1392) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6793 (pt0) cc_final: 0.6132 (pp20) REVERT: A 17 LYS cc_start: 0.7711 (pptt) cc_final: 0.7053 (ptpt) REVERT: A 203 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.3970 (tt) REVERT: B 13 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: B 15 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7107 (ttmm) REVERT: B 23 LYS cc_start: 0.8152 (tttp) cc_final: 0.7616 (tmtm) REVERT: B 42 ARG cc_start: 0.7828 (tpt170) cc_final: 0.7457 (tpt170) REVERT: B 44 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: B 46 ARG cc_start: 0.8584 (mmt-90) cc_final: 0.8226 (mmp80) REVERT: B 59 TYR cc_start: 0.9246 (OUTLIER) cc_final: 0.8089 (t80) REVERT: B 134 ARG cc_start: 0.7870 (ptp-110) cc_final: 0.7232 (ppp80) REVERT: B 146 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8689 (tp) REVERT: B 155 ASN cc_start: 0.8949 (t0) cc_final: 0.8726 (t0) REVERT: B 217 MET cc_start: 0.8829 (ppp) cc_final: 0.8450 (pmm) REVERT: B 298 ASP cc_start: 0.9129 (t0) cc_final: 0.8814 (t0) REVERT: G 36 ASP cc_start: 0.8610 (m-30) cc_final: 0.8199 (m-30) REVERT: R 41 GLU cc_start: 0.5752 (mm-30) cc_final: 0.5332 (tt0) REVERT: R 376 ARG cc_start: 0.5498 (OUTLIER) cc_final: 0.4477 (mmp80) REVERT: R 407 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7722 (m-40) REVERT: P 9 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6421 (mp0) outliers start: 30 outliers final: 13 residues processed: 152 average time/residue: 0.6871 time to fit residues: 111.0961 Evaluate side-chains 150 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 351 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 420 TRP Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.197958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.109531 restraints weight = 10014.011| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.11 r_work: 0.2927 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10429 Z= 0.221 Angle : 0.598 7.914 14154 Z= 0.323 Chirality : 0.045 0.156 1564 Planarity : 0.005 0.062 1805 Dihedral : 4.999 35.591 1403 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.05 % Allowed : 17.08 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1261 helix: 1.44 (0.23), residues: 530 sheet: 0.08 (0.32), residues: 233 loop : -0.26 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 20 TYR 0.020 0.002 TYR R 148 PHE 0.016 0.002 PHE B 151 TRP 0.014 0.002 TRP B 339 HIS 0.005 0.002 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00504 (10422) covalent geometry : angle 0.59446 (14142) SS BOND : bond 0.00297 ( 6) SS BOND : angle 2.17848 ( 12) hydrogen bonds : bond 0.04811 ( 492) hydrogen bonds : angle 4.37418 ( 1392) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6826 (pt0) cc_final: 0.6238 (pp20) REVERT: A 17 LYS cc_start: 0.7783 (pptt) cc_final: 0.7163 (ptpt) REVERT: A 203 LEU cc_start: 0.4814 (OUTLIER) cc_final: 0.4340 (tt) REVERT: B 13 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: B 23 LYS cc_start: 0.8179 (tttp) cc_final: 0.7606 (tmtm) REVERT: B 42 ARG cc_start: 0.7698 (tpt170) cc_final: 0.7348 (tpt170) REVERT: B 44 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: B 59 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8264 (t80) REVERT: B 134 ARG cc_start: 0.7872 (ptp-110) cc_final: 0.7220 (ppp80) REVERT: B 146 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8757 (tp) REVERT: B 197 ARG cc_start: 0.8884 (mtp180) cc_final: 0.8645 (mtm110) REVERT: B 217 MET cc_start: 0.8814 (ppp) cc_final: 0.8409 (pmm) REVERT: B 298 ASP cc_start: 0.9234 (t0) cc_final: 0.8946 (t0) REVERT: B 340 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8491 (m110) REVERT: G 36 ASP cc_start: 0.8665 (m-30) cc_final: 0.8278 (m-30) REVERT: G 59 ASN cc_start: 0.8257 (t0) cc_final: 0.8010 (t0) REVERT: R 376 ARG cc_start: 0.5547 (OUTLIER) cc_final: 0.4415 (mmp80) REVERT: R 407 ASN cc_start: 0.8118 (OUTLIER) cc_final: 0.7751 (m-40) REVERT: P 9 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6255 (mp0) outliers start: 33 outliers final: 14 residues processed: 146 average time/residue: 0.6709 time to fit residues: 103.9119 Evaluate side-chains 146 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 303 MET Chi-restraints excluded: chain R residue 351 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.200514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113316 restraints weight = 10058.666| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.15 r_work: 0.2976 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10429 Z= 0.116 Angle : 0.496 5.006 14154 Z= 0.269 Chirality : 0.041 0.152 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.591 33.331 1403 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.40 % Allowed : 17.73 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.24), residues: 1261 helix: 1.70 (0.23), residues: 534 sheet: 0.22 (0.33), residues: 228 loop : -0.26 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 20 TYR 0.019 0.001 TYR R 148 PHE 0.013 0.001 PHE A 212 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00251 (10422) covalent geometry : angle 0.49440 (14142) SS BOND : bond 0.00231 ( 6) SS BOND : angle 1.51080 ( 12) hydrogen bonds : bond 0.03933 ( 492) hydrogen bonds : angle 4.08616 ( 1392) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6712 (pt0) cc_final: 0.6073 (pp20) REVERT: A 17 LYS cc_start: 0.7727 (pptt) cc_final: 0.7031 (ptpt) REVERT: A 203 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4263 (tt) REVERT: A 265 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: B 23 LYS cc_start: 0.8144 (tttp) cc_final: 0.7606 (tmtm) REVERT: B 42 ARG cc_start: 0.7801 (tpt170) cc_final: 0.7457 (tpt170) REVERT: B 44 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: B 46 ARG cc_start: 0.8592 (mmt-90) cc_final: 0.8239 (mmp80) REVERT: B 59 TYR cc_start: 0.9232 (OUTLIER) cc_final: 0.7994 (t80) REVERT: B 134 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7188 (ppp80) REVERT: B 146 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8687 (tp) REVERT: B 197 ARG cc_start: 0.8838 (mtp180) cc_final: 0.8601 (mtp85) REVERT: B 217 MET cc_start: 0.8852 (ppp) cc_final: 0.8459 (pmm) REVERT: B 298 ASP cc_start: 0.9161 (t0) cc_final: 0.8845 (t0) REVERT: G 36 ASP cc_start: 0.8596 (m-30) cc_final: 0.8269 (m-30) REVERT: R 41 GLU cc_start: 0.5743 (mm-30) cc_final: 0.5316 (tt0) REVERT: R 376 ARG cc_start: 0.5464 (OUTLIER) cc_final: 0.4512 (mmp80) REVERT: R 381 PHE cc_start: 0.6267 (t80) cc_final: 0.5867 (t80) REVERT: R 407 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: R 414 ARG cc_start: 0.6131 (mmp-170) cc_final: 0.4927 (mmt90) REVERT: P 9 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6282 (mp0) outliers start: 26 outliers final: 10 residues processed: 142 average time/residue: 0.7028 time to fit residues: 105.9519 Evaluate side-chains 143 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 351 LYS Chi-restraints excluded: chain R residue 365 VAL Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain R residue 407 ASN Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 0.0020 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 36 optimal weight: 0.0970 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 40.0000 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 0.0370 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.202857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116706 restraints weight = 10099.217| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.80 r_work: 0.3103 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10429 Z= 0.094 Angle : 0.465 4.979 14154 Z= 0.251 Chirality : 0.040 0.145 1564 Planarity : 0.004 0.064 1805 Dihedral : 4.231 34.120 1403 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.66 % Allowed : 18.84 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.24), residues: 1261 helix: 1.95 (0.23), residues: 538 sheet: 0.33 (0.32), residues: 228 loop : -0.13 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.019 0.001 TYR R 148 PHE 0.013 0.001 PHE A 212 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00198 (10422) covalent geometry : angle 0.46384 (14142) SS BOND : bond 0.00170 ( 6) SS BOND : angle 1.26961 ( 12) hydrogen bonds : bond 0.03478 ( 492) hydrogen bonds : angle 3.87667 ( 1392) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6660 (pt0) cc_final: 0.6194 (pp20) REVERT: A 17 LYS cc_start: 0.7827 (pptt) cc_final: 0.7189 (ptpt) REVERT: A 203 LEU cc_start: 0.4402 (OUTLIER) cc_final: 0.3981 (tt) REVERT: A 265 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8122 (ttm110) REVERT: A 392 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8458 (mt-10) REVERT: B 23 LYS cc_start: 0.8142 (tttp) cc_final: 0.7658 (tmtm) REVERT: B 42 ARG cc_start: 0.7723 (tpt170) cc_final: 0.7344 (tpt170) REVERT: B 44 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: B 46 ARG cc_start: 0.8471 (mmt-90) cc_final: 0.8164 (mmp80) REVERT: B 76 ASP cc_start: 0.8582 (p0) cc_final: 0.8312 (p0) REVERT: B 134 ARG cc_start: 0.7880 (ptp-110) cc_final: 0.7277 (ppp80) REVERT: B 146 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8549 (tp) REVERT: B 197 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8587 (mtp85) REVERT: B 217 MET cc_start: 0.8793 (ppp) cc_final: 0.8410 (pmm) REVERT: B 298 ASP cc_start: 0.9033 (t0) cc_final: 0.8698 (t0) REVERT: G 36 ASP cc_start: 0.8572 (m-30) cc_final: 0.8158 (m-30) REVERT: N 43 LYS cc_start: 0.8559 (mttp) cc_final: 0.8355 (mtmm) REVERT: R 41 GLU cc_start: 0.5729 (mm-30) cc_final: 0.5316 (tt0) REVERT: R 232 LEU cc_start: 0.7087 (tp) cc_final: 0.6393 (mm) REVERT: R 293 ASP cc_start: 0.7230 (t0) cc_final: 0.6772 (t70) REVERT: R 354 LEU cc_start: 0.8611 (mp) cc_final: 0.8383 (mt) REVERT: R 376 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.4597 (mmp80) REVERT: R 381 PHE cc_start: 0.6415 (t80) cc_final: 0.6090 (t80) REVERT: R 414 ARG cc_start: 0.6264 (mmp-170) cc_final: 0.5015 (mmt90) REVERT: P 9 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6551 (mp0) outliers start: 18 outliers final: 5 residues processed: 143 average time/residue: 0.6901 time to fit residues: 104.7774 Evaluate side-chains 131 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.201437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113856 restraints weight = 10065.410| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.85 r_work: 0.3058 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10429 Z= 0.106 Angle : 0.486 6.706 14154 Z= 0.261 Chirality : 0.041 0.153 1564 Planarity : 0.004 0.064 1805 Dihedral : 4.305 34.833 1403 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.57 % Allowed : 19.76 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1261 helix: 2.08 (0.23), residues: 532 sheet: 0.40 (0.32), residues: 235 loop : -0.13 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 20 TYR 0.019 0.001 TYR R 148 PHE 0.014 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00229 (10422) covalent geometry : angle 0.48393 (14142) SS BOND : bond 0.00202 ( 6) SS BOND : angle 1.44445 ( 12) hydrogen bonds : bond 0.03674 ( 492) hydrogen bonds : angle 3.89300 ( 1392) Misc. bond : bond 0.00004 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.6661 (pt0) cc_final: 0.6177 (pp20) REVERT: A 17 LYS cc_start: 0.7810 (pptt) cc_final: 0.7111 (ptpt) REVERT: A 203 LEU cc_start: 0.4413 (OUTLIER) cc_final: 0.3990 (tt) REVERT: B 23 LYS cc_start: 0.8176 (tttp) cc_final: 0.7674 (tmtm) REVERT: B 42 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7366 (tpt170) REVERT: B 44 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: B 46 ARG cc_start: 0.8549 (mmt-90) cc_final: 0.8217 (mmp80) REVERT: B 101 MET cc_start: 0.9102 (mtp) cc_final: 0.8887 (mtp) REVERT: B 134 ARG cc_start: 0.7851 (ptp-110) cc_final: 0.7228 (ppp80) REVERT: B 146 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8671 (tp) REVERT: B 197 ARG cc_start: 0.8849 (mtp180) cc_final: 0.8629 (mtp85) REVERT: B 217 MET cc_start: 0.8797 (ppp) cc_final: 0.8409 (pmm) REVERT: B 298 ASP cc_start: 0.9054 (t0) cc_final: 0.8727 (t0) REVERT: G 36 ASP cc_start: 0.8594 (m-30) cc_final: 0.8244 (m-30) REVERT: R 41 GLU cc_start: 0.5729 (mm-30) cc_final: 0.5313 (tt0) REVERT: R 232 LEU cc_start: 0.7167 (tp) cc_final: 0.6482 (mm) REVERT: R 293 ASP cc_start: 0.7226 (t0) cc_final: 0.6793 (t70) REVERT: R 354 LEU cc_start: 0.8616 (mp) cc_final: 0.8399 (mt) REVERT: R 376 ARG cc_start: 0.5534 (OUTLIER) cc_final: 0.4548 (mmp80) REVERT: R 381 PHE cc_start: 0.6506 (t80) cc_final: 0.6207 (t80) REVERT: R 414 ARG cc_start: 0.6170 (mmp-170) cc_final: 0.4919 (mmt90) REVERT: R 418 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: P 9 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6485 (mp0) outliers start: 17 outliers final: 9 residues processed: 135 average time/residue: 0.6853 time to fit residues: 98.3247 Evaluate side-chains 139 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 30 VAL Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 376 ARG Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain P residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 0.0030 chunk 87 optimal weight: 50.0000 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.201475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.113983 restraints weight = 10137.405| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.83 r_work: 0.3056 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 10429 Z= 0.144 Angle : 1.014 59.146 14154 Z= 0.535 Chirality : 0.041 0.243 1564 Planarity : 0.004 0.063 1805 Dihedral : 4.319 34.830 1403 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.75 % Allowed : 19.58 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.24), residues: 1261 helix: 2.09 (0.23), residues: 532 sheet: 0.40 (0.32), residues: 235 loop : -0.16 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 20 TYR 0.018 0.001 TYR R 148 PHE 0.014 0.001 PHE A 212 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00293 (10422) covalent geometry : angle 1.01273 (14142) SS BOND : bond 0.00248 ( 6) SS BOND : angle 1.83783 ( 12) hydrogen bonds : bond 0.03752 ( 492) hydrogen bonds : angle 3.89531 ( 1392) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.54 seconds wall clock time: 93 minutes 57.11 seconds (5637.11 seconds total)